Projects

Anthropology

Network analysis of example Crow-Omaha and other kinship systems.

The Division of Anthropology at the AMNH has recently begun to rely on the use of tools more familiar in biological evolution and systematics due to advances in both data acquisition and databasing, and interpretive models based on a tree/network framework. The research of Anthropology curator Peter Whiteley employs an anthro-informatic approach, utilizing computational and phylogenetic tools to build on databases of human kinship variants, and test hypotheses about kinship system transformation and evolution.

Astrophysics

LH 95 stellar nursery in Large Magellanic Cloud. Credit: NASA/ESA.

Research in the Department of Astrophysics includes a major component of computational work. Led by Division Chair, Mordecai Mac Low, the group studies the formation of planets, and stars, and the effects of supernova explosions on interstellar gas, with applications to galactic winds and galaxy formation. They use numerical gas dynamical and magnetohydrodynamical (MHD) simulations as a primary tool.

Current Studies

  • Planet Formation
  • Turbulence in Protoplanetary disks
  • Star formation
  • Galactic Winds

Spotlight

Planet Formation

is believed to take place in the disks of gas and dust around forming stars. The earliest stages of that process occurs while the gas is moving through the disk and falling onto the star. This is known as accretion, and while we can observe it occurring, we do not have good theoretical insight into what is causing it. The most promising agent of accretion is turbulence driven by the magnetorotational instability. This turbulence is critical in understanding the dynamics of the gas and dust, the latter of which creates the seeds for planet formation. We are using the parallel computing facility at AMNH to make detailed turbulence models under a variety of conditions that might occur in protoplanetary disks. Having a medium sized facility--larger than a standard workstation but smaller than the largest supercomputers--allows us to make many, many small scale models. This in turn allows us to explore the parameter space before investing significant amounts of time on the largest supercomputing facilities.

-Jeff Oishi

Systematic Biology

Focus Areas

  • Viral Evolution
  • Expressed sequence tag analysis
  • Phylogenetic and evolutionary relationships
  • Reconstruction patterns of gene rearrangements

The biological science divisions of the AMNH (Invertebrate Zoology, Vertebrate Zoology, and Paleontology) are involved in a broad variety of research projects concerning the evolutionary relationships of creatures of immense diversity, ranging from viruses, foraminifera, and sponges to arthropods, and vertebrates. The basic problem of reconstructing evolutionary trees falls into a class of problems known at NP-hard, i.e. non-deterministic polynomial-time hard. Researchers in these divisions are at the forefront of algorithmic innovation and implementation of combinatoric heuristics.

Researchers in the Invertebrate Zoology Division, lead by Chair Ward Wheeler have developled a series of heuristics to the tree-alignment problem and chromosomal alignment with moves. These ideas (and other existing approaches) have been implemented in our open source, freely available POY version 4 software (Varon et al., 2010; ), which was preceded by MALIGN.

Malign

The multiple alignment procedures implemented in MALIGN are close parallels to those used to search for minimum length cladograms. The logic and program commands will be clear to those familiar with programs such as Hennig86, NONA, and PAUP. Alignment topologies are constructed via different sequences and improved through branch swapping. Each alignment topology yields a multiple alignment and cladograms are constructed from that alignment. The cost of the most parsimonious cladogram is then assigned as the multiple alignment cost.

Download

Current version: 2.7

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Source code

Documentation

Test files

POY

Phylogenetic Analysis of DNA and other data using dynamic homology

POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood). A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.

To receive news, and ask questions that you may have, join the POY mailing list.

The development of POY4 is sponsored in part by CIPRES.

Download

Current version: 5.0.0 Alpha (December 2011)

Citation

Varón, A., L. S. Vinh, W. C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, 26:72-85.

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Current version: 4.1.2 (7 August 2009)

Citation

Varón, A., L. S. Vinh, W. C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, 26:72-85.

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Old versions of POY

Version 4.1.1 (23 January 2009)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.1.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.1 (15 November 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0.2911 (7 October 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2911. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0.2885 (15 August 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2885. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0.2870 (21 May 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2870. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 2635 (11 March 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2635. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 2602 (8 February 2008)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2602. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 2398 (23 October 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2398. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 2318 (12 October 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2318. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 2205 (10 September 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2205. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 1983 (18 July 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1983. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 1908 (12 June 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1908. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 1902 (11 June 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1902. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 1724 (29 March 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1724. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 4.0 Beta build 1665 (17 February 2007)

Citation

Varón, A., L. S. Vinh, I. Bomash, W. C. Wheeler. 2008. POY 4.0 Beta 1665. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

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Version 3.0.11

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Related software

Version 3.0

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Related software

Version 2.7

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Version 2.0

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Sample Files

Sample data for DOS

Sample data for Linux

Sample matrices

Sample output

Utilities

jack2hen

Converts POY output (one or more trees in nested parentheses format) into a matrix (in hennig format) of group inclusion characters representing the concensus tree used for contraint files.

Datasets

Datasets for published studies are available here for download. Descriptions of datasets and formats for each study are provided in the associated readme files.

Arango, C. P., and W. C. Wheeler. 2007. Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology. Cladistics 23:00-00: 0-00.

Grant, T., D. R. Frost, J. P. Caldwell, R. Gagliardo, C. F. B. Haddad, P. J. R. Kok, B. D. Means, B. P. Noonan, W. Schargel and W. C. Wheeler. 2006. Phylogenetic systematics of dart-poison frogs and their relatives (Anura: Athesphatanura: Dendrobatidae). Bulletin of the American Museum of Natural History 299: 1-262.

Frost, D.R., T. Grant, J. Faivovich, R. Bain, A. Haas, C.F.B. Haddad, R.O. de Sá, S.C. Donnellan, C.J. Raxworthy, M. Wilkinson, A. Channing, J.A. Campbell, B.L. Blotto, P. Moler, R.C. Drewes, R.A. Nussbaum, J.D. Lynch, D. Green, and W.C. Wheeler. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297: 1-370.